[2024-01-24 12:47:18,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:18,185] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:18,185] [INFO] DQC Reference Directory: /var/lib/cwl/stge55b688d-179d-4850-8c76-d8aa1f400da8/dqc_reference
[2024-01-24 12:47:19,398] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:19,399] [INFO] Task started: Prodigal
[2024-01-24 12:47:19,399] [INFO] Running command: gunzip -c /var/lib/cwl/stgaea4e0ff-0661-46fb-8183-d1c8d5908d56/GCF_007197575.1_ASM719757v1_genomic.fna.gz | prodigal -d GCF_007197575.1_ASM719757v1_genomic.fna/cds.fna -a GCF_007197575.1_ASM719757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:32,612] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:32,613] [INFO] Task started: HMMsearch
[2024-01-24 12:47:32,613] [INFO] Running command: hmmsearch --tblout GCF_007197575.1_ASM719757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge55b688d-179d-4850-8c76-d8aa1f400da8/dqc_reference/reference_markers.hmm GCF_007197575.1_ASM719757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:32,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:32,951] [INFO] Found 6/6 markers.
[2024-01-24 12:47:32,996] [INFO] Query marker FASTA was written to GCF_007197575.1_ASM719757v1_genomic.fna/markers.fasta
[2024-01-24 12:47:32,997] [INFO] Task started: Blastn
[2024-01-24 12:47:32,997] [INFO] Running command: blastn -query GCF_007197575.1_ASM719757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge55b688d-179d-4850-8c76-d8aa1f400da8/dqc_reference/reference_markers.fasta -out GCF_007197575.1_ASM719757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:34,230] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:34,234] [INFO] Selected 18 target genomes.
[2024-01-24 12:47:34,235] [INFO] Target genome list was writen to GCF_007197575.1_ASM719757v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:34,243] [INFO] Task started: fastANI
[2024-01-24 12:47:34,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea4e0ff-0661-46fb-8183-d1c8d5908d56/GCF_007197575.1_ASM719757v1_genomic.fna.gz --refList GCF_007197575.1_ASM719757v1_genomic.fna/target_genomes.txt --output GCF_007197575.1_ASM719757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:47,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:47,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge55b688d-179d-4850-8c76-d8aa1f400da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:47,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge55b688d-179d-4850-8c76-d8aa1f400da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:47,581] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:47,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:47,582] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	100.0	1364	1364	95	conclusive
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	82.231	826	1364	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	82.1087	580	1364	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	80.0134	601	1364	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	79.9634	621	1364	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	79.6143	510	1364	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	79.5829	497	1364	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	79.4369	453	1364	95	below_threshold
Ornithinimicrobium flavum	strain=CPCC 203535	GCA_004526345.1	1288636	1288636	type	True	79.2454	491	1364	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.2216	484	1364	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	79.0958	471	1364	95	below_threshold
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	79.0217	455	1364	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	78.8131	462	1364	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	78.1332	297	1364	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	78.1238	309	1364	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	77.9522	320	1364	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	77.8592	322	1364	95	below_threshold
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	77.7015	267	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:47,583] [INFO] DFAST Taxonomy check result was written to GCF_007197575.1_ASM719757v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:47,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:47,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:47,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge55b688d-179d-4850-8c76-d8aa1f400da8/dqc_reference/checkm_data
[2024-01-24 12:47:47,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:47,626] [INFO] Task started: CheckM
[2024-01-24 12:47:47,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007197575.1_ASM719757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007197575.1_ASM719757v1_genomic.fna/checkm_input GCF_007197575.1_ASM719757v1_genomic.fna/checkm_result
[2024-01-24 12:48:57,109] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:57,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:57,133] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:57,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:57,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007197575.1_ASM719757v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:57,135] [INFO] Task started: Blastn
[2024-01-24 12:48:57,135] [INFO] Running command: blastn -query GCF_007197575.1_ASM719757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge55b688d-179d-4850-8c76-d8aa1f400da8/dqc_reference/reference_markers_gtdb.fasta -out GCF_007197575.1_ASM719757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:58,918] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:58,924] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:58,925] [INFO] Target genome list was writen to GCF_007197575.1_ASM719757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:58,937] [INFO] Task started: fastANI
[2024-01-24 12:48:58,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea4e0ff-0661-46fb-8183-d1c8d5908d56/GCF_007197575.1_ASM719757v1_genomic.fna.gz --refList GCF_007197575.1_ASM719757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007197575.1_ASM719757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:09,997] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:10,017] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:10,017] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_007197575.1	s__Ornithinicoccus sp007197575	100.0	1364	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012515595.1	s__Ornithinicoccus sp012515595	82.6044	715	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121625.1	s__Ornithinicoccus cavernae	82.237	825	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352835.1	s__Ornithinicoccus muralis	82.0957	581	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716185.1	s__Ornithinicoccus hortensis	79.9389	621	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004322775.1	s__Serinicoccus sp004322775	79.4316	520	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	79.3826	458	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004526345.1	s__Serinicoccus flavus	79.3057	488	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577095.1	s__Ornithinimicrobium sp003577095	79.2057	408	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009602535.1	s__Ornithinicoccus_A halotolerans	79.1386	425	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386315.1	s__Serinicoccus marinus	78.9315	453	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	98.28	97.42	0.92	0.87	4	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.5996	399	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	78.1327	297	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190805.1	s__Flexivirga oryzae	78.0567	310	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003724155.1	s__Flexivirga caeni	77.7015	267	1364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:10,019] [INFO] GTDB search result was written to GCF_007197575.1_ASM719757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:10,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:10,027] [INFO] DFAST_QC result json was written to GCF_007197575.1_ASM719757v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:10,027] [INFO] DFAST_QC completed!
[2024-01-24 12:49:10,027] [INFO] Total running time: 0h1m52s